Carpenter syndrome is a congenital disorder mainly characterized by craniosynostosis – soft spots of the skull fuse prematurely resulting in skull elongation. MEGF8, a protein in the MEGF8-MGRN1-MOSMO (MMM) regulatory complex involved in Hedgehog (Hh) signaling, has been previously linked to Carpenter syndrome. Hh signaling, a core developmental pathway, plays many roles in skull development, including functioning as a guidance cue for cranial neural crest cells (foundational cells for skull bones) and regulating bone ossification (bone hardening). Despite the previous research linking MEGF8 and anomalous skull development, the role of the MMM complex and Hh signaling in skull development and the mechanism behind this abnormal skull development is still widely unknown. I’m exploring the mechanism by which elevated Hh signaling influences cell fates during the development of skull structures. I investigated a whole-embryo knockout mouse model to identify regions where overexpression of Hh correlates to abnormal skull phenotypes. I explored and measured these phenotypes via imaging a genetic Hedgehog reporter mouse line and skeletal stained embryos of various ages. These knockout mice were embryonic lethal because of a congenital heart defect associated with loss of Hh. We introduced an inducible Cre to conditionally knockout the MMM complex at a later age, avoiding heart defects. My findings identified the interparietal and parietal regions of the skull as areas of interest, visualized by over-ossification and lack of defined structural boundaries- nasal and palatal development was normally observed. These findings suggest that elevated Hh signals result in abnormal development of skull structures, similar to craniosynostosis, and are involved in intramembranous ossification (skull structures) rather than endochondral ossification (nasal/palate). From these findings, I’m investigating how Hh signaling plays a role in skull development and intramembranous ossification.

Transcriptional repression plays a critical role in the regulation of various biological processes, including developmental pathways and disease progression. Corepressors are proteins recruited by partner proteins to negatively influence the transcription of genes. TPL is a corepressor from the model plant Arabidopsis thaliana, and is known to play a pivotal role in transcriptional repression. My project aims to identify other proteins that work with TPL to form a transcriptional repression complex at a single engineered locus. To further understand the function of corepressors, we built a synthetic repressor system, dCas9-TPL, designed to specifically repress the transcription of the RUBY reporter gene. When expressed, the RUBY reporter turns Arabidopsis thaliana pink. In previous phases of this research, we utilized the EMS (ethyl methanesulfonate) mutagenesis protocol to create a population of plants containing many random mutations. Screening these plants for increased RUBY expression, I successfully Identified promising homozygous lines where plants demonstrated bright pink flowers and unique phenotypes such as early flowering, light avoidance, and small stature. Last quarter, I sent five lines to be sequenced and each line displayed distinct mutations that I can further explore to pinpoint the exact TPL interactor responsible for its unique phenotype. I am also investigating known TPL interactors such as SPT4, SPT5, and MED21 by creating transgenic lines within my control dCas9-TPL + RUBY line. Through genetic screening, I have validated the phenotypes among these control experiments. By investigating the intricate network of interactions between these regulatory proteins, I aim to gain a deeper understanding of how gene expression is coordinated across different cell types and how this process controls complex developmental pathways.

The Eastern North Pacific gray whales (Eschrichtius robustus) have a long migration from their breeding grounds in Mexico to their feeding grounds in Alaska. A subgroup of the Eastern North Pacific stock, nicknamed the Sounders, deviate from the migratory path most gray whales follow to feed in the Salish Sea, typically between the months of March and May. Other studies show that gray whales feed on benthic organisms such as ghost shrimp. Studies conducted in the Arctic area of the gray whale migration route have seen sea ice playing an important role in the gray whales being able to enter the areas where they feed. One working hypothesis is that gray whale shifts in migration patterns are the direct result of climate change; this could explain why some of the Eastern North Pacific gray whales enter and feed in Possession Sound. I analyzed sightings data, shared by the Whale Museum and recorded in Possession Sound, WA from 2000-2022. These data, most of which were compiled by the Orca Network, were filtered to identify the number of visitations each month over the study period. Early analysis shows a phenological shift in the time of the gray whale's arrival and departure from Possession Sound. The shift shows an increase in the number of months gray whales are present in Possession Sound, from a March to May visit to a year-round presence. Although these results cannot explain the reason for the phenological shift, future research must look into related shifts in the Arctic ice formation as well as ambient air and water temperature shifts. Future research calculating density of ghost shrimp in Possession Sound will also indicate why this location is favored.

Zostera marina (eelgrass) is one of the many important biological features of Possession Sound, acting as a substrate for many microorganisms, a filter of greenhouse gases, and as protection for many species. The Possession Sound has been marked as a Seagrass Sanctuary by the Department of Natural Resources, which protects and monitors nearshore eelgrasses within the basin. By looking at what kinds of species are found in a marine environment, researchers can assess an ecosystem's overall health. Environmental DNA (eDNA) is a data capture technique used by researchers that picks up DNA traces left behind by organisms, and shows their presence/absence in a given area. The study site, Mount Baker Terminal, lies inside the Possession Sound basin near Everett, Washington, and contains a large eelgrass bed. I collected 10 samples using passive filters submerged at various depths inside and outside the eelgrass bed in 2024 and processed at a WDFW lab. I analyzed these data and 40 additional samples collected by the Ocean Research College Academy from 2021-2024 using similar methods. I hypothesized that there would be more species such as crustaceans, fish, and other plants inside the eelgrass because of its ability to protect and maintain a nutrient-dense environment. These data will help shed light on species richness in each environment, which has potential implications for understanding the overall health of the ecosystem and the critical role eelgrass plays in the estuary.

Possession Sound, located between the city of Everett and Whidbey Island, is a part of both a key economic area and a bustling marine environment. Because of the marine activity, scientists study all sorts of parameters involving the water including noise. Numerous studies have assessed ambient noise in marine environments to investigate the influence of tidal forces on ambient noise. These reports found that tidal noise or “flow noise” is observed around the 0-100Hz range with the most significant impacts observed centered around 25hz. The Ocean Research College Academy operates a SoundTrap ST400 STD hydrophone mounted to Mount Baker Terminal that takes recordings daily for most of the year. Mount Baker Terminal is a small marine terminal operated by the Port of Everett, located just north of the town of Mukilteo. Using data collected from the hydrophone, I took measurements of ambient noise in root mean square amplitude centered around the 25hz range and compared that to NOAA tidal data at Everett, Washington. Using these data I investigated the potential presence of a relationship between the tides and ambient noise. When the initial measurements of root mean square amplitude were compared to tidal data from the area the results showed that tides had no significant impact on the ambient noise at Mount Baker Terminal. Investigating the effects of tides on ambient noise can be crucial to future acoustic research done by researchers in the area as results could be affected by noise created or affected by tides. Future analysis should investigate the impacts of other natural contributors to the soundscape such as rain and wind.

Ocean acidification is the reduction of pH in seawater due to increased carbon dioxide from fossil fuels in the atmosphere and other anthropogenic factors. Ocean acidification causes shellfish such as oysters to experience difficulty building their shells. Acidification trends in the North Pacific Basin are well documented, yet pH trends in Possession Sound, a salt-wedge estuary located in the Salish Sea is less documented. Possession Sound receives discharge from the Snohomish River and has human activity along the shoreline. In this study, the average change of pH in the middle of the North Pacific Ocean was measured and compared to the average change of pH in Possession Sound since 2016. I analyzed data collected from ARGOS Floats located in the central North Pacific Ocean. For Possession Sound, I used data collected from a  YSI EXO Sonde in partnership with the Ocean Research College Academy (ORCA). I collected data on 12 research cruises in 2024. I expect to find a slightly greater decrease in pH within Possession Sound than the North Pacific Basin due to the additional anthropogenic factors present in the Sound. Preliminary analysis shows a slight seasonal change in pH in Possession Sound, but little to no change yearly. I expect the data to show a steady decrease in pH for Possession Sound and the North Pacific Ocean basin every year since 2016. Calculating acidification rates and learning how they differ in various geographical locations, with separate factors, will increase understanding of the impacts of ocean acidification, which may be used in conservation efforts. 

Acetaminophen (APAP) is a widely used over-the-counter drug known for its analgesic and antipyretic properties. Several clinical factors can influence how APAP is absorbed, distributed, metabolized and excreted from the body (i.e., its pharmacokinetics (PK)). APAP is metabolized into several metabolites, including APAP-glucuronide, APAP-sulfate, APAP-cysteine, and APAP-N-acetylcysteine. Therefore, accurately determining plasma concentrations of APAP and its metabolites is crucial for understanding how individuals metabolize APAP and environmental influences on APAP PK. To address this, I am reproducing a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay to determine concentrations of APAP and its metabolites in plasma. I analyzed plasma samples collected from seven healthy volunteers following oral administration of 500 mg of APAP. To prepare the samples, I added 70 μL of diluted internal standard mix into the tubes containing 30 μL of plasma. Samples were centrifuged and the supernatants were transferred clean tubes and dried down with nitrogen gas. Samples were reconstituted in mobile phase for analysis using LC-MS/MS. I analyzed the LC-MS/MS data to calculate the plasma concentration vs. time curves for each analyte. I used Phoenix WinNonlin to estimate key PK parameters, including peak concentration (Cmax), time of peak concentration (Tmax), clearance, half-life, volume of distribution, and area under the curve (AUC). This LC-MS/MS assay provides a platform for precise quantification of APAP and its metabolites, and will be essential for our lab’s future studies on the impact of the gut microbiome on APAP’s PK.

The introduction of harmful strains of Escherichia coli (E. coli) in the marine environment negatively impacts ecosystem health. When unnatural strains of E. coli are introduced through pollution events, spikes in animal sickness and death occur, and harm to human health is more likely. Understanding relationships among parameters known for contributing harmful strains of E.coli and parameters more likely to contribute non-harmful strains is important to identify the most impactful parameters leading to harmful E. coli events. Possession Sound, WA is an ideal study site for monitoring multiple parameters associated with the introduction of E. coli to a saltwater environment. The study site includes the second largest freshwater input in Puget Sound, the Snohomish River, which passes many farms on its way to the Sound. The study site is also surrounded by a heavily industrialized port, and a large-density population center. I collected water samples at various depths and recorded animal presence from 2023-2025 at ten separate sites. Using a sterile procedure, I plated water samples onto bacterial plates using Easygel® agar. Overflow and river discharge data were provided by the city of Everett and USGS respectively. Historical data were collected following similar protocols by the Ocean Research College Academy. I hypothesized that increased presence of E. coli would strongly correlate with high river discharge events and combined sewer overflow events more than other inputs, but early analysis does not support this correlation. Further research must consider parameters such as residence time of E. coli, lag time after discharge events, and water chemistry characteristics. 

Gray whales in the North Pacific annually migrate north to the Gulf of Alaska and the Bering Sea, and their migration route bypasses the Salish Sea. Roughly a dozen of these whales, commonly called “the Sounders,” have detoured their migration into North Puget Sound since the 1990s. These whales have been observed feeding on ghost shrimp in the intertidal area of sediment beaches in North Puget Sound, using a high risk strategy of feeding on shrimp at high tides. This feeding strategy leaves large indents, or “feeding pits”, in the sediment that are revealed at low tide and can provide insight into the Sounders’ feeding habits and contribute to a deeper understanding of the North Pacific gray whale population. My research focused on locational trends of gray whale feeding pits on Jetty Island West beach, and I observed longitudinal locations of specific pits in the intertidal zone to investigate feeding patterns. I observed feeding pits with drone imagery collected at low tide and compiled into aerial maps, or “orthomosaics,” and I compared feeding pits in different longitudes to observe where on the beach whales are feeding. Two seasons of feeding pit imagery were collected from late winter and spring of 2024 and 2025, and I have analyzed the imagery using ArcGIS pro. Survey site area ranged from approximately 0.09km² to 0.4 km² for different maps. The non-invasive nature of drone photogrammetry has recently increased its use in marine and biological research, and this method of data collection is ideal for surveying gray whale pits on Jetty Island. Because of the increased risk of feeding in higher tidal zones, I expect to find higher concentrations of feeding pits at lower tidal zones.

Eelgrass meadows (Zostera spp.) and Kelp forests (Nereocystis spp.) are both essential habitats in Possession Sound, a saltwater estuary formed where the Snohomish River meets the Salish Sea. Home to many marine species, the Possession Sound has unique salinity levels that provide a rich environment to support marine life. These ecosystems provide vital services such as helping clean the water, sheltering fish, absorbing or filtering carbon, producing oxygen, and protecting coastlines. Given the rich marine habitat that develops in eelgrass meadows and kelp forests, conducting a study of the organisms that reside in the habitat would be beneficial to learn about their condition and influence on life within Possession Sound. To conduct the study, I used eDNA sampling for data collection. eDNA sampling analyzes genetic material from organisms and identifies what species are present in a given environment. I collected samples from two ecosystems at the stations closest to each habitat. MBT (eelgrass) and Kelp Sanctuary (kelp forest). The data I collected from the two sites were sent to the molecular genetics laboratory at WDFW for metabarcoding analysis to identify species using a passive filtration protocol. The data were then combined with historic data to determine the species present in both habitats, specifically focusing on fish and crustacean species. Preliminary analysis suggests that these habitats have similar organisms that frequent each habitat. I expect to see this trend reflected in additional eDNA data, meaning the eelgrass meadows and kelp forests will have similar representative species.

Noise pollution from 10 Hz to 200 kHz disrupts marine life and importantly damages cetaceans’ ability to navigate surroundings, communicate, and hunt. Possession Sound supports gray, humpback, and orca whales who all pass through its congested waterways and underwater soundscape. During 2023-2024 a voluntary slow down of commercial vessels occurred in Puget Sound. The results from Quiet Sound showed that 71% of 795 commercial vessels slowed down through the marked zones. There was a 50% 3 dB decrease in sound created and resulted in 72 additional minutes when underwater noise did not reach over 110 dB. One location where noise pollution is prominent is between the city of Mukilteo and the town of Clinton on Whidbey Island. The Mukilteo-Clinton ferries run 21 and a half hours a day, leading them to be a regular contributor to the underwater soundscape and an important factor to assess our environment's health. This study was conducted using data from a SoundTrap 400 hydrophone mounted .4 miles from the Mukilteo ferry terminal. 168 hours of constant data have been gathered between 2021 and 2024. From 1:30 am to 4:40 am, ferries don't run. Noise levels when the ferries don't run were compared to when they do run, which proved to show a significant reduction in overall RMS amplitude. Graphs plotting constant 24-hour RMS amplitude show spikes every half hour, which lines up with the Washington State Ferries (WSF) departure schedule. Future research must identify specific sound frequency signatures for the ferries and compare those frequencies and amplitudes to known values that may harm cetaceans and other marine life.

Queer Silence is a video essay born out of my utter fascination with silence in cinema. This is not to be mistaken with silent-era cinema, but instead the use of silence in sound films – an artistic technique that could not be applied until sound and film were synchronized. Once sound became unified with moving images, its absence became a powerful and versatile method for enhancing emotional and artistic expression onscreen. I explore cinematic silence in this project through videographic criticism: a research method that deploys audiovisual techniques to critically analyze and reflect on audiovisual media. This relatively new form of scholarship differs significantly from traditional written analysis or even a recorded lecture, allowing meanings to emerge through the critic’s reconfiguration of images, sounds, and text. In this way, the video essay offers the perfect method for analyzing quiet moments in film; I directly experiment with the relationship between image and silence. What began as an exercise exploring silence as an element of dialogue in Céline Sciamma’s Portrait of a Lady on Fire (2019) blossomed into an exploration of the vast, complicated, and entrancing applications of silence within a selection of contemporary queer films. Indeed, to be queer is to be all too familiar with silence; silencing your own sexuality (or having it silenced by others), silent longing for recognition and acceptance, or even the desire for silence in the noise of the heteronormative world. These quiet moments in the daily lives of queer communities are thus reflected in queer media; they become an exchange of unspoken words and an expression of intricate emotions, demanding deep contemplation from the audience. It is within these films that one truly understands that queer silence isn’t really silence at all – and it is time to start listening.

A trigger warning included in the opening sequence of Blink Twice (2024), an American psychological thriller directed by Zoë Kravitz, motivates this research project. Trigger warnings are a controversial topic of debate. While some critics exalt their positive benefits for minorities and PTSD, others argue they "spoil" the material and/or perpetuate a victim mentality. Trigger warnings originated as a cautionary device prefacing personal accounts of trauma in online spaces for sexual abuse survivors, and are now commonly found on college campuses, streaming services, and other content driven spaces. In recent years, trigger warnings have appeared on the big screen, inserted directly after the MPA rating. It is unusual to find a preface of this sort in a horror film, a genre that draws an audience through depictions of graphic violence and representations of trauma. The project employs the tools of videographic criticism-a critical rearrangement of images, sounds, and words-to assess Blink Twice as a retrospective exploration of feminine representation in horror. My audiovisual essay, "Red Rabbits," traces the lineage of Kravitz's film by concentrating on three influential periods in the study of horror: canonical horror of the 1970s, feminist critiques of sexualized violence in the 1990s, and the contemporary landscape of the #MeToo movement. Taking the historical context of the film into consideration elicits questions of necessity, purpose, and impact of the trigger warning. "Red Rabbits" employs multiscreen, superimposition, and intertitles to explore how the text that prefaces this female-directed horror film informs and affects the viewing experience. Rather than offer an answer to ongoing debates, or insist on a singular perspective, "Red Rabbits" implores its viewer to investigate their own perceptions of the trigger warning's role in both the instance of Blink Twice and in modern culture. 

Nearly all forms of cardiac disease are characterized by cardiac fibrosis, which contributes to heart failure and arrhythmias due to the accumulation of collagen deposits. Collagen, a crucial extracellular matrix (ECM) protein, is secreted by cardiac fibroblasts—the primary cell type responsible for generating this stiff scar tissue known as fibrosis. Fibroblasts are highly plastic cells that can transition between quiescent and activated states. The Davis Lab has developed a minimally invasive intermittent injury model to cyclically stress cardiac fibroblasts in vivo, allowing for a deeper investigation into the role of cellular memory in regulating the fibrotic response. Notably, we can reduce fibrotic remodeling in this model by inhibiting p38 gene function in the activated population, thereby encouraging a shift back to a quiescent state. My work aims to determine whether the once-activated population is proliferating at the second injury stimulus as well, or if a new population of fibroblasts is proliferating with repeat injury. To address this, I am utilizing genetic lineage tracing and Click-iT EdU technology, which allows for precise biolabeling while also preserving cell morphology and integrity by integrating into the cell's DNA. I am also performing immunohistochemistry staining to detect other proteins of interest that will serve as proliferation markers as well. Based on prior findings in the Davis Lab, we hypothesize that once-activated fibroblasts will go on to activate again when exposed to repeated disease stimuli, but there will be no second wave of proliferation as there was no change in total fibroblast number. 

Congenital hydrocephalus is a condition that is characterized by an accumulation of cerebrospinal fluid in the brain. This increases pressure in the brain, leading to neurological deficits. Surgery is the only current intervention however, even after surgery, patients experience lifelong complications. The underlying genetic mechanisms that cause human hydrocephalus are still unknown. To investigate the mechanisms behind hydrocephalus, the lab developed a mouse model by selectively ablating Notch signaling in specific brain regions. These mice developed obstructive hydrocephalus due to a loss of cell adhesion in the Sylvian aqueduct, a thin channel connecting the 3rd and 4th ventricles of the brain. Interestingly, brain regions exposed to high levels of Hedgehog signaling retained cell adhesion, indicating a possible protective role. Based on this, I hypothesized that Hedgehog signaling plays an unexpected role in supporting Notch-mediated cell adhesion. To test this hypothesis, I utilized small molecule Notch inhibitors to suppress Notch signaling activity in cortical spheroids. Cortical spheroids are precursors to cortical organoids derived from mouse embryonic stem cells. Preliminary data showed that various concentrations of different inhibitors were able to reduce cell adhesion and disrupt neural rosette formation in the spheroids. Neural rosettes are structures that recapitulate early cortical formation. After treatment with Hedgehog agonists, there was an increase in the number of neural rosettes in both untreated and inhibitor-treated spheroids, indicating that Hedgehog signaling can compensate for a loss of Notch signaling and preserve cell adhesion in the developing brain. These results seem to suggest that Hedgehog signaling can compensate for a loss of Notch through cell adhesion maintenance and prevent premature neural progenitor cell differentiation. The goal of the project is to establish cortical spheroids as a model system to screen potential genes associated with human hydrocephalus along with future drug therapies.
 

Harbor seals (Phoca vitulina) are one of the most prevalent marine mammals along the West Coast of the United States. In the Salish Sea, harbor seal populations have increased significantly since the Marine Mammal Protection Act of 1972, and the population is now considered to be at carrying capacity. These seals prey on many species of fish and invertebrates and are themselves a major component of the diet of local transient killer whales. Harbor seals can frequently be seen resting in groups on land at places called haul-out sites. They are known for their high site fidelity, meaning that the same seals consistently return to the same sites. These haul-out sites are frequently dominated by a specific sex or age range. This study investigated whether specific seals are more likely to be re-sighted in smaller groups or with other specific individuals within the haul-out site. Using SealNet, an AI facial recognition system, I analyzed photographic data from 750 images from the Ocean Research College Academy’s (ORCA’s) long-term data collection that were taken from haul-out sites at the mouth of the Snohomish River. SealNet identifies individual seals by analyzing facial features and comparing them across photos, assigning a similarity score for each photo and ranking them in descending order. The results of this research are aimed at determining if harbor seals exhibit more complex social structures within haul-out sites. Understanding the social structure of harbor seals can help provide insight into their cooperation, competition, and overall population dynamics. This study focuses on haul-out sites while the majority of interactions occur in the water, so further study is needed to better understand the dynamics of this population.

The pigeon guillemot (Cepphus columba) is an under-researched member of the Alcidae family found in the northern Pacific Ocean. While there have been significant findings on the individualization of terrestrial birds and predominantly endangered alcids, there is a severe lack of call documentation and analysis for pigeon guillemots. This creates a large gap in the avian communities’ awareness of these birds’ communications on their own and in groups, as well as for the species as a whole. The purpose of this study is to gain a deeper understanding of the significance of pigeon guillemot vocalizations within the Possession Sound, and to answer the question of how pigeon guillemot vocalizations vary between groups and individuals. Recordings of vocalizations were taken with a handheld microphone aboard Ocean Research College Academy’s research vessel in the Possession Sound within the last year. Some recordings sourced from Xeno Canto outside of the Possession Sound were utilized, but a large portion have been taken via boat and from land by hand. Analysis of calls was conducted in RavenPro, Excel, and Rstudio to compare components of calls such as frequency, duration, and variation. Through this preliminary research, there is a noticeably wide range of variety in the frequency and duration of calls within groups. Call patterns are highly varied during recording events in which multiple pigeon guillemots are present, with recognizable patterns of call formations. Out of my 20 recordings, with 10 being shore-based and 10 being boat-based, 4 distinct call types have been identified, and further research is needed.

Everett’s Naval base, train tracks running parallel to the shore, and robust recreational/commercial boat traffic add to the increasingly loud acoustic environment of Possession Sound. Several studies have linked elevated sound pressure levels to reducing the acoustic communication space and disrupting critical behaviors such as feeding, breeding, and communication in marine fish and invertebrates. Ongoing research within the Salish Sea has highlighted some habitats like seagrass meadows (Zostera marina) and kelp forests (Nereocystis spp.) that can aid in mitigating the effects of noise pollution on underwater communities on top of being a foraging habitat, shelter, and critical nurseries for various species. Although the Salish Sea as a whole has seen dwindling kelp forests and eelgrass meadows in recent years, Possession Sound nonetheless contains both habitats. For my study, both Z. marina and N. ssp. were present around the perimeter of Hat Island, 5 nautical miles from the Port of Everett. I collected 8 seven minute recordings using a deployable hydrophone (SoundTrap 300). Preliminary analysis has revealed distinct biological sounds, primarily within the 0-5 kHz range, and are denoted as a part of the biophony of the soundscape. I analyzed the soundscapes using ‘Root Mean Square’ (RMS) amplitude formatting, because it indicates the equivalent steady state energy value of oscillating sound waves. I utilized RMS amplitude measurements for comparison inside the habitats to the appropriate counterpart outside the habitats (exclusion zone is a minimum distance of 100 meters from the previous recording). Future analysis will expand with continued gathering of ambient soundscape data into early spring to ensure the utilized dataset can represent multiple seasons and atmospheric conditions as well.

Learner experiences are under-examined in environmental learning research. Our research consists of studies of experiential aspects of environmental learning by undergraduate researchers, conducted over three years, culminating in a focus on how community-engaged learning (CEL) fosters connections between social justice, ecological consciousness, and student well-being. Research questions we came to consider were: What connections are students drawing between social justice and ecological consciousness? How does engaging in community-based environmental learning affect students’ well-being? Methods such as coding, memoing, reflecting through learning diaries, whole-part-whole analysis, and group collaboration all contributed to establishing an adaptable infrastructure of undergraduate research (UGR) in experiential aspects of the course. Our findings on students’ connections between social justice and ecological consciousness revealed their thoughts about becoming advocates, or “leaning toward justice”, though they had diverse prior knowledge and experiences. Findings on the CEL experience within the large course with regard to well-being showed how students integrate environmental education with community engagement, particularly in addressing issues such as food insecurity, environmental justice, and language barriers for immigrant communities. Some key themes found were that CEL promoted personal growth through unexpected learning, connection to nature & emotional relief, and a sense of belonging in research participants’ experiences. The significance of this research has been to establish a way for undergraduate researchers to drive experiential learning research, and to find research outcomes about how learning experiences foster awareness of social and ecological justice, encouraging students to see themselves as advocates for change. 

The Hedgehog signaling pathway is essential for embryonic development. Errors in the Hedgehog pathway can cause limb, heart, and left-right patterning defects. However, Hedgehog signaling also plays a crucial role in the regeneration and maintenance of adult tissues and cells. Mutations in key components can lead to the constitutive activation of the pathway, leading to uncontrolled cell proliferation and cancer. Dysregulated Hedgehog signaling is associated with two major cancer types: basal cell carcinoma (skin cancer) and medulloblastoma (a pediatric brain tumor). To counteract this, small molecule inhibitors like Vismodegib have been developed to directly bind to and suppress the activity of the Hedgehog transducer, Smoothened (SMO). While Vismodegib is a potent inhibitor of Hedgehog signaling, mutations in SMO eventually lead to drug resistance and tumor relapse.The mechanisms underlying Vismodegib drug resistance and how the Hedgehog signaling pathway is reactivated in its presence remains unknown. To investigate these mechanisms, a constitutively active fluorescent Hedgehog reporter was knocked into the mouse skin cells, and a genome-wide CRISPR knockout (KO) library approach was used to generate a pool of gene-edited cells. Following treatment with the Hedgehog ligand Sonic Hedgehog (SHH) to activate the pathway and Vismodegib to inhibit it, fluorescence-activated cell sorting (FACS) was performed to sort the cells with high fluorescence to identify the KO cells that retained Hedgehog pathway activity after treatment with the Hedgehog inhibitor. This screen identified 10 novel genes associated with Vismodegib resistance. For further studies, I used a dual guide approach to generate knockouts of each gene respectively and clone them into CRISPR/Cas9 gene-editing vectors. My goal is to evaluate the expression of different Hedgehog genes using biochemical approaches. This would allow us to understand how each gene affects downstream pathway activity and identify the mechanism through which these genes could potentially impart drug resistance.

Disruption of the Wnt signaling pathway is critical in the emergence of some of the most difficult cancers to treat. Transducin β-like protein 1 (TBL1) forms a complex with β-catenin, a transcription factor that switches ON Wnt target genes (Li & Wang, 2008). The Nemhauser Lab engineered a synthetic repressor circuit, dCas9-TBL1, that targets a constructed constitutive promoter driving GFP expression in human cells. I hypothesize that levels of TBL1 activity will correlate strongly with expression of Wnt target genes. My research uses time course qPCR to test Wnt-induced gene expression in both HEK293 and HCT15 cell lines. HEK293 have normal levels of Wnt signaling, whereas the HCT15 colon cancer cell line is known to have high Wnt activity which contributes to uncontrolled cell growth. Specifically, I will extract RNA from both cell types at 6, 24, and 48 hours after treatment with a control chemical and test for expression levels of  Wnt-target genes such as AXIN2. These experiments will test whether the elevation of downstream Wnt-target gene expression is correlated negatively or positively with TBL1 activity, and will enable further understanding of this route to oncogenesis and future optimization of chemotherapy targets.

Schizophrenia is a complex mental illness influenced by genetic, environmental, and neurodevelopmental factors. Cognitive impairments are a prominent symptom of schizophrenia and are associated with long-term outcomes. Current literature suggests that damaging genetic risk factors, such as copy number variations (CNVs) and loss of function (LOF) mutations, are important contributors to schizophrenia etiology and may influence cognitive functioning among patients. However, isolating the effects of these variants can be complicated by the contributions of other factors, such as environmental factors, to schizophrenia etiology and functioning among patients. Using a within-family study design offers one way to control for background factors and isolate the effects of rare, damaging risk variants. This study used data from 446 subjects enrolled in the University of California, Los Angeles Family Study, involving 83 schizophrenia and 59 control families with genetic and behavioral data. An initial analysis of variance (ANOVA) revealed that schizophrenia probands showed a significantly greater decrease in IQ compared to their own relatives than control probands compared to their own relatives. Building on these findings, this study aims to explore whether extreme within-family IQ differences are associated with the presence of known risk CNVs for schizophrenia and broader neurodevelopmental disorders or LOF mutations in genes previously associated with these disorders. By elucidating the heterogeneity of schizophrenia through the examination of genetic risk variants and their connection to cognitive impairments, this research may help inform optimal intervention strategies for different patients and thereby improve clinical outcomes for individuals with schizophrenia and related disorders.

Corepressors are an essential element of gene repression – complexes of proteins that keep genes off, yet poised to turn on when needed. Clarifying the mechanism of this repression is key to understanding gene regulation in all eukaryotes in diseased and non-diseased states. My project is implementing a forward genetic screen in Arabidopsis thaliana to identify and characterize proteins that bind to and regulate the conserved plant corepressor TPL. TPL is fully essential to plant development, so to visualize TPL inhibition in living plants, we created an Arabidopsis line containing a synthetic repressor, TPL fused to dCas9(dCas9-TPL), that represses RUBY, a genetic reporter that turns Arabidopsis plants dark pink. Plants with both constructs appear light pink as dCas9-TPL represses RUBY expression. Mutations in proteins needed to maintain TPL-based repression lead to dark pink plants, allowing us to identify mutants to study. Using ethyl methanesulfonate (EMS), we created a pool of seeds with random point mutations and the repressed RUBY construct. My team and I visually screened the mutated pool for pink plants showing inhibited RUBY repression and successfully identified promising homozygous mutants with unique phenotypes including infertility, shade avoidance, and irregular growth patterns. Using whole genome sequencing and computational analysis, I selected specific loci to further investigate. We are currently testing our candidate mutants' sensitivity to the plant hormone auxin, one of the best-understood TPL-regulated pathways. My next steps will be to identify the causal mutation through the following: (1) characterizing additional mutations in the same gene to compare phenotypes using available mutant libraries, (2) testing whether the candidate gene interacts with TPL using assays like yeast two-hybrid, and (3) complementing my mutants with wild-type versions of candidate genes. By uncovering new proteins, I aim to piece together more of TPL's conserved mechanism of repression. 

This research examines the statistical interactions of genetic risk scores and behavior data from wearable devices, including physical activity and sleep measures, to predict Major Depressive Disorder (MDD) symptom onset. MDD is a widespread mental health issue, with nearly all indicators of mental health worsening from 2013 to 2023 and 30% or more current children experiencing mental health symptoms. Research shows that lifestyle changes, such as improving physical activity and sleep behavior, can alleviate early-stage MDD symptoms. But, many people are unaware of their genetic vulnerability to MDD, leaving them unprepared for potential challenges. This study uses the Adolescent Brain Cognitive Development (ABCD) dataset, the largest U.S. longitudinal study of brain development and child health. ABCD provides extensive psychometric, demographic, genetic, and wearable data for research. This study uses genetic and wearable tracking data to predict MDD severity and support early interventions. It also investigates how genetic risk levels inform how physical activity and sleep patterns must change to mitigate MDD symptom severity.  This study will calculate polygenic risk scores (PRS) for ABCD subjects and improve prediction accuracy for non-European populations using state-of-the-art bioinformatics tools. Then, this study will utilize mixed effects modeling to analyze additive and interactive effects of PRS, wearable data, and depression severity scores. Lastly, this study will program machine learning (ML) models to provide variable importance and accuracy results. The goal is to create a personalized, data-driven approach to MDD prevention and empower individuals to take proactive steps toward mental well-being based on a comprehensive view of their genetic and behavioral factors.

Students often face academic pressure, interpersonal issues, and employment challenges during the transition into college. While 48.9% of undergraduate students face depressive symptoms (Luo et. al, 2024) and 52% of students report anxiety significantly inhibiting their academic performance (Crosswell et al), only 15% of students with mental illness utilize college mental health resources (Jaisoorya, 2021). To overcome conflicting schedules, stigma, and limited accessibility, we investigate whether self-regulated mindfulness practices would reduce anxiety and depression symptoms in college students. Participants were instructed to practice guided meditation videos daily. Depression and anxiety were measured through Qualtrics using the Beck Depression Inventory (BDI) (Beck et al., 1996) and Generalized Anxiety Questionnaire (APA) (Spitzer, et al., 2006) before and after a 2-week meditation practice. We hypothesize that regular mindfulness meditation practices moderately reduce anxiety and depression in college students. 

All cells have a stochastic component to their gene expression, such that even when in the same environment, there will be cell-to-cell differences in gene expression. Studies of this variability in gene expression dynamics have been limited by technological capabilities for measuring gene expression history with single-cell resolution. We have built a history-dependent integrase recorder of gene expression with single-cell resolution in the model plant Arabidopsis thaliana to study the impact of cell-to-cell gene expression variation in two contexts: development of side or lateral roots (LRD) and root regeneration (RR). The recorder uses integrases, proteins from bacteriophages that mediate permanent, heritable DNA changes based on the presence and orientation of a pair of integrase sites. Fluorescent reporter genes within the target construct allows for expression of fluorescent proteins associated with sequential expression of developmental genes. The recorder allows us to tie the switching to expression of developmental genes by expressing integrases with developmental promoters for genes that guide root differentiation. Utilizing our recorder, we are able to illuminate and evaluate variation in the recorder output among roots growing in different contexts. We hypothesize that regeneration leads to more heterogeneity in gene expression than lateral root development, as the latter has more standardized initial conditions and consistent local cues to constrain transcriptional dynamics. We aim to investigate connections between larger scale anatomical variation and underlying cell-to-cell gene expression heterogeneity. This technology will allow us to further understand the dynamics of gene expression during root development and could unlock new avenues for agricultural research and engineering.

The auxin hormone is necessary for many essential plant functions. Corepressors from the TPX family hold auxin response genes (ARGs) OFF unless auxin levels are high. TPX proteins are brought to ARGs through interaction with Aux/IAA adaptor proteins, which can bind to auxin-regulated transcription factors. Plant pathogens interfere with the auxin transcriptional pathway, making a plant more susceptible to infection. Oomycetes, for example, are a common plant pathogen commonly found as a mold growing on ripe tomatoes and strawberries. Oomycetes inject RxLR effector proteins into plant cells to reprogram the immune response. RxL21 is one of these effectors, and it contains a binding site for TPX proteins that is very similar to what is found in the Aux/IAA proteins. We hypothesize that RxL21 competes with Aux/IAA for recruitment of TPX proteins and keeps auxin genes on during an infection. I tested this hypothesis by performing a cytoplasmic split ubiquitin assay (Cyto-SUS), which is a protein-protein interaction assay done in yeast. Through this assay, we detected weaker TPX-Aux/IAA interaction when RxL21 was present, suggesting that competition for TPX protein interaction is occurring. I also tested whether the RxL21 competition would alter transcription of an ARG using a fluorescence-based assay in yeast. I observed much greater fluorescence when RxL21 was present, suggesting that RxL21 competition with Aux/IAA for recruitment of TPX results in increased transcription of ARG. In future experiments, I will further test our hypothesis by expressing RxL21 and other effector proteins in specific cell types in the model plant Arabidopsis thaliana. These experiments will allow me to quantify the impact of the competition for TPX corepressors on a developmental process. The results of this work could guide the design of new, broad-spectrum strategies to protect plants from pathogens.

All organisms regulate genes for proper cell development, healthy environmental response, and prevention of disease. One way to regulate genes is through transcriptional repression, specifically through corepressors that bind to repressors to inhibit expression of genes. The TPL/TPR corepressor family is crucial in Arabidopsis thaliana for regulating auxin-dependent genes during embryogenesis, root and shoot axis formation, differentiation, and environmental responses. Due to functional redundancy among the TPL/TPR gene family, partial mutations in the family do not create full loss of function. However, knocking out multiple family members is lethal. My research aims to induce loss of function for TPL in specific tissue. To achieve this, I started with a plant strain that is mutated for three of the five family members through insertional mutagenesis by T-DNA, leading to a partial loss of function, with two remaining genes remaining functional. Then I constructed a single TPL copy under the control of an integrase-based molecular switch, which when expressed, inverts the promoter of the TPL gene, turning it off. This construct, assembled through Golden Gate cloning, includes a YFP-tagged TPL gene and an mScarlet reporter that allows me to confirm TPL expression (YFP) or its absence (mScarlet) through fluorescence microscopy. I have integrated this construct with the controllable TPL switch into Arabidopsis, and my next goal is to use a CRISPR/Cas9 system to mutate the remaining two TPL genes for full loss of function. I will then utilize the integrase control switch system for specific TPL repression in the lateral roots. Such a study helps synthetic biologists understand the necessity of TPL in specific tissues, avoiding full knockout lethality. With corepressors existing among different eukaryotes, this study has broader implications in understanding human repressors, such as TBL-1 that are linked to dysregulation of gene expression in diseases like cancer.